6TSF | pdb_00006tsf

Crystal structure of human L ferritin (HuLf) Fe(III)-loaded for 60 minutes

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5LG8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	293	80 mM cadmium nitrate, 80 mM ammonium sulfate, 200 mM sodium acetate, pH 4.6

Crystal Properties
Matthews coefficient	Solvent content
3.59	65.72

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 151.14	α = 90
b = 151.14	β = 90
c = 151.14	γ = 90

Symmetry
Space Group	I 4 3 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2018-02-19	M	MAD
2	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2018-02-19	M	MAD
3	1	x-ray	100	PIXEL	DECTRIS PILATUS3 6M		2018-02-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97622	Diamond	I03
2	SYNCHROTRON	DIAMOND BEAMLINE I03	1.73891	Diamond	I03
3	SYNCHROTRON	DIAMOND BEAMLINE I03	1.74478	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.09	106.87	93.5	0.065	0.069	0.015	1	26.8	20.3		16631		2	42.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.09	2.2	100		0.849	0.887	0.19	0.925	3.7	21.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	5LG8	2.09	47.84	16500	823	92.848	0.211	0.2087	0.21	0.252	0.25	44.84

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.38
r_dihedral_angle_4_deg	25.739
r_dihedral_angle_3_deg	17.642
r_lrange_it	11.001
r_lrange_other	10.848
r_scangle_it	8.946
r_scangle_other	8.945
r_scbond_it	6.323
r_scbond_other	6.319
r_dihedral_angle_1_deg	5.857
r_mcangle_it	5.556
r_mcangle_other	5.552
r_mcbond_it	4.231
r_mcbond_other	4.187
r_angle_other_deg	2.439
r_angle_refined_deg	1.858
r_nbd_other	0.262
r_symmetry_nbd_refined	0.254
r_nbd_refined	0.252
r_symmetry_nbd_other	0.215
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.171
r_chiral_restr	0.17
r_symmetry_xyhbond_nbd_refined	0.137
r_metal_ion_refined	0.104
r_symmetry_nbtor_other	0.078
r_bond_other_d	0.036
r_bond_refined_d	0.014
r_gen_planes_other	0.01
r_symmetry_xyhbond_nbd_other	0.009
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1382
Nucleic Acid Atoms
Solvent Atoms	145
Heterogen Atoms	17

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing